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Leveraging BrainSeq data, we constructed ancestry-stratified expression quantitative trait locus (eQTL) maps for 71,022 transcriptional non-coding enhancer (TNE) RNAs. By integrating the latest Psychiatric Genomics Consortium (PGC3) schizophrenia GWAS with European-ancestry population-based eQTLs via Summary-data-based Mendelian Randomization (SMR), we identified 61 schizophrenia-risk TNEs, 19 of which overlapped with those from differential expression (DE) analysis. Intriguingly, for 19 overlapping TNEs, effects from DE analysis were inversely correlated with SMR effects (r\u2009=\u2009\u22120.57,\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20090.01), attributable to the opposing contributions of phenotype and genotype to TNE expression (r\u2009=\u2009\u22120.78,\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20092.96E\u22123). We further linked this discrepancy to reduced levels of the repressor ZNF135 in schizophrenia, which derepressed motif-matched TNEs. Finally, we identified and experimentally validated that an enhancer RNA within the intronic region of RGS6, termed RGS6e, regulates the expression of genes associated with the nervous system through trans-acting mechanisms, promoting neuronal differentiation and thereby reducing the risk of schizophrenia, consistent with the SMR results. This study underscores the significance of eQTL-based SMR analysis in elucidating the role of enhancers and their transcriptional products in schizophrenia risk. The eQTL map of TNEs developed in our study holds considerable potential for application in enhancer research related to other mental diseases or neurodegenerative diseases, thereby enhancing our understanding of how enhancers contribute to disease pathogenesis and progression.\n                  <\/jats:p>","DOI":"10.1038\/s41380-025-03358-6","type":"journal-article","created":{"date-parts":[[2025,11,23]],"date-time":"2025-11-23T08:25:09Z","timestamp":1763886309000},"page":"2133-2143","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Mendelian randomization facilitates identification of schizophrenia risk enhancer RNAs"],"prefix":"10.1038","volume":"31","author":[{"given":"Linyan","family":"Ye","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaoying","family":"Ni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renhao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyao","family":"Che","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2428-6165","authenticated-orcid":false,"given":"Fu","family":"Xiong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6116-4584","authenticated-orcid":false,"given":"Cunyou","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0098-6100","authenticated-orcid":false,"given":"Zhongju","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,11,23]]},"reference":[{"key":"3358_CR1","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1038\/s41586-022-04434-5","volume":"604","author":"V Trubetskoy","year":"2022","unstructured":"Trubetskoy V, Pardi\u00f1as AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, et al. 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